| 'MiscMetabar' package | MiscMetabar-package |
| Plot accumulation curves for 'phyloseq-class' object | accu_plot |
| Plot accumulation curves with balanced modality and depth rarefaction | accu_plot_balanced_modality |
| Compute the number of sequence to obtain a given proportion of ASV in accumulation curves | accu_samp_threshold |
| Add information from 'blast_pq()' to the 'tax_table' slot of a _phyloseq_ object | add_blast_info |
| Add dna in 'refseq' slot of a 'physeq' object using taxa names and renames taxa using prefix_taxa_names and number (default Taxa_1, Taxa_2 ...) | add_dna_to_phyloseq |
| Add information about Guild for FUNGI the FUNGuild databse | add_funguild_info |
| Add information to sample_data slot of a phyloseq-class object | add_info_to_sam_data |
| Add new taxonomic rank to a phyloseq object. | add_new_taxonomy_pq |
| Permanova on a phyloseq object A wrapper for the 'vegan::adonis2()' function in the case of 'physeq' object. | adonis_pq |
| Permanova (adonis) on permutations of rarefaction even depth | adonis_rarperm_pq |
| Run Aldex on a phyloseq object | aldex_pq |
| List the size of all objects of the GlobalEnv. | all_object_size |
| Run ANCOMBC2 on phyloseq object | ancombc_pq |
| Test if the mean number of sequences by samples is link to the modality of a factor | are_modality_even_depth |
| Transform the otu_table of a 'phyloseq-class' object into a 'phyloseq-class' object with a binary otu_table. | as_binary_otu_table |
| Assign taxonomy using blastn algorithm and the blast software | assign_blastn |
| Assign taxonomy with dada2 using 2 steps assignTaxonomy and assignSpecies | assign_dada2 |
| A wrapper of 'IdTaxa' | assign_idtaxa |
| Assign taxonomy using MMseqs2 | assign_mmseqs2 |
| Assign Taxonomy using Sintax algorithm of Vsearch | assign_sintax |
| Assign taxonomy using LCA | assign_vsearch_lca |
| Visualization of two samples for comparison | biplot_pq |
| Blast all sequence of 'refseq' slot of a 'phyloseq-class' object against a custom database. | blast_pq |
| Blast some sequence against sequences from of a 'derep-class' object. | blast_to_derep |
| Blast some sequence against 'refseq' slot of a 'phyloseq-class' object. | blast_to_phyloseq |
| Build phylogenetic trees from refseq slot of a phyloseq object | build_phytree_pq |
| Detect for chimera taxa using vsearch | chimera_detection_vs |
| Search for a list of sequence in an object to remove chimera taxa using vsearch | chimera_removal_vs |
| Plot OTU circle for 'phyloseq-class' object | circle_pq |
| Clean phyloseq object by removing empty samples and taxa | clean_pq |
| Compare samples in pairs using diversity and number of ASV including shared ASV. | compare_pairs_pq |
| Count sequences in fasta or fastq file | count_seq |
| Cumulative Sum Scaling (CSS) normalization of a phyloseq object | css_pq |
| Remove primers using cutadapt | cutadapt_remove_primers |
| Fungal OTU in phyloseq format | data_fungi |
| Fungal OTU in phyloseq format | data_fungi_mini |
| Fungal OTU in phyloseq format | data_fungi_sp_known |
| Compute different functions for different class of vector. | diff_fct_diff_class |
| Compute paired distances among matrix (e.g. otu_table) | dist_bycol |
| Calculate ecological distance among positive controls vs distance for all samples | dist_pos_control |
| Distribution of sequences across a factor for one taxon | distri_1_taxa |
| Compute Hill diversity numbers for all samples in an OTU table | divent_hill_matrix_pq |
| Translates a factor into colors. | fac2col |
| Fastp: adapter detection, quality control and preprocessing of FASTQ files | fastp |
| Convert FASTQ file(s) to FASTA file(s) | fastq_to_fasta |
| Filter taxa of a phyloseq object based on the minimum number of sequences/samples | filt_taxa_pq |
| Filter taxa by cleaning taxa with NA at given taxonomic rank(s) | filt_taxa_wo_NA |
| Filter undesirable taxa using blast against a custom database. | filter_asv_blast filter_taxa_blast |
| A wrapper of the function 'dada2::filterAndTrim()' to use in targets pipeline | filter_trim |
| Find the MMseqs2 binary | find_mmseqs2 |
| Find the vsearch binary | find_vsearch |
| Format a fasta database in dada2 format | format2dada2 |
| Format a fasta database in dada2 format for Species assignment | format2dada2_species |
| Format a fasta database in sintax format | format2sintax |
| Create a visualization table to describe taxa distribution across a modality | formattable_pq |
| Assign Guilds to Organisms Based on Taxonomic Classification | funguild_assign |
| Funky palette color | funky_color |
| Get the extension of a file | get_file_extension |
| Retrieve the FUNGuild database | get_funguild_db |
| Alluvial plot for taxonomy and samples factor vizualisation | ggaluv_pq |
| Box/Violin plots for between-subjects comparisons of Hill Number | ggbetween_pq |
| Scatterplot with marginal distributions and statistical results against Hill diversity of phyloseq object | ggscatt_pq |
| Venn diagram of 'phyloseq-class' object using 'ggVennDiagram::ggVennDiagram' function | ggvenn_pq |
| Automated model selection and multimodel inference with (G)LMs for phyloseq | glmutli_pq |
| Geometric Mean of Pairwise Ratios (GMPR) normalization of a phyloseq object | gmpr_pq |
| Performs graph-based permutation tests on phyloseq object | graph_test_pq |
| Hill diversity accumulation curve for a phyloseq object (default: q = 1) | hill_acc_pq |
| Bar plot of Hill diversity with SE, jittered points, and Kruskal-Wallis test | hill_bar_pq |
| Hill Diversities and Corresponding Accumulation Curves for phyloseq | hill_curves_pq |
| Graphical representation of hill number 0, 1 and 2 across a factor | hill_pq |
| Test multiple times effect of factor on Hill diversity with different rarefaction even depth | hill_test_rarperm_pq |
| Calculate hill number and compute Tuckey post-hoc test | hill_tuckey_pq |
| iNterpolation and EXTrapolation of Hill numbers (with iNEXT) | iNEXT_pq |
| Install MMseqs2 from GitHub releases | install_mmseqs2 |
| Install vsearch binary | install_vsearch |
| Test if blastn is installed. | is_blastn_installed |
| Test if cutadapt is installed. | is_cutadapt_installed |
| Test if falco is installed. | is_falco_installed |
| Test if fastp is installed. | is_fastp_installed |
| Test if krona is installed. | is_krona_installed |
| Check whether MMseqs2 is installed and callable | is_mmseqs2_installed |
| Test if MultiQC is installed. | is_multiqc_installed |
| Test if mumu is installed. | is_mumu_installed |
| Test if swarm is installed. | is_swarm_installed |
| Test if vsearch is installed. | is_vsearch_installed |
| Make Krona files using KronaTools. | krona |
| Compute and test local contributions to beta diversity (LCBD) of samples | LCBD_pq |
| A wrapper of 'DECIPHER::LearnTaxa()' | learn_idtaxa |
| Run LEfSe on a phyloseq object | lefser_pq |
| List fastq files | list_fastq_files |
| Load a phyloseq object from an RData file written by 'save_pq()' or 'write_pq()' | load_pq |
| Post Clustering Curation of Amplicon Data. | lulu |
| Lulu reclustering of class 'physeq' | lulu_pq |
| Depth-robust alpha diversity residuals (McKnight / Mikryukov) | mcknight_residuals_pq |
| Merge Krona files using KronaTools. | merge_krona |
| Merge samples by a sample variable or factor | merge_samples2 merge_samples2,otu_table-method merge_samples2,phyloseq-method merge_samples2,sample_data-method |
| Merge taxa in groups (vectorized version) | merge_taxa_vec merge_taxa_vec,otu_table-method merge_taxa_vec,phylo-method merge_taxa_vec,phyloseq-method merge_taxa_vec,taxonomyTable-method merge_taxa_vec,XStringSet-method |
| Deprecated function(s) in the MiscMetabar package | adonis_phyloseq biplot_physeq clean_physeq ggVenn_phyloseq hill_phyloseq hill_tuckey_phyloseq lulu_phyloseq MiscMetabar-deprecated otu_circle physeq_graph_test plot_deseq2_phyloseq plot_edgeR_phyloseq read_phyloseq sankey_phyloseq summary_plot_phyloseq venn_phyloseq write_phyloseq |
| Recluster sequences of a phyloseq object or cluster a list of DNA sequences using MMseqs2 software | mmseqs2_clustering |
| Visualization of a collection of couples of samples for comparison | multi_biplot_pq |
| Test and plot multipatt result | multipatt_pq |
| Multiple plot function | multiplot |
| Plot taxonomic distribution across 3 taxonomic levels and optionally one sample factor | multitax_bar_pq |
| MUMU reclustering of class 'physeq' | mumu_pq |
| Discard legend in ggplot2 | no_legend |
| Normalize OTU table using samples depth | normalize_prop_pq |
| Convert a value (or a fraction x/y) in percentage | perc |
| Convert phyloseq OTU count data into DGEList for edgeR package | phyloseq_to_edgeR |
| Export a phyloseq object to GBIF MDT template CSV/TSV files | phyloseq_to_MDT_csv |
| Export a phyloseq object to a multi-sheet Excel file for GBIF MDT submission | phyloseq_to_MDT_excel |
| Return a DNAStringSet object from either a character vector of DNA sequences or the 'refseq' slot of a phyloseq-class object | physeq_or_string_to_dna |
| Plot ANCOMBC2 result for phyloseq object | plot_ancombc_pq |
| Plot kmer complexity of references sequences of a phyloseq object | plot_complexity_pq |
| Plot DESeq2 results for a phyloseq or a DESeq2 object. | plot_deseq2_pq |
| Plot edgeR results for a phyloseq or a edgeR object. | plot_edgeR_pq |
| Plot information about Guild from tax_table slot previously created with 'add_funguild_info()' | plot_guild_pq |
| Plot and test local contributions to beta diversity (LCBD) of samples | plot_LCBD_pq |
| Plot the result of a mt test 'phyloseq::mt()' | plot_mt |
| A wrapper of plot_ordination with vegan distance matrix | plot_ordination_pq |
| Overview plot of alpha and beta diversity for a phyloseq object | plot_overview_pq |
| Plot the nucleotide proportion at both extremity of the sequences | plot_refseq_extremity_pq |
| Plot the nucleotide proportion of references sequences | plot_refseq_pq |
| Plot species contributions to beta diversity (SCBD) of samples | plot_SCBD_pq |
| A diagnostic plot of the number of sequences per samples | plot_seq_ratio_pq |
| Plot taxonomic distribution in function of a factor with stacked bar in % | plot_tax_pq |
| Plot a tsne low dimensional representation of a phyloseq object | plot_tsne_pq |
| Plot the partition the variation of a phyloseq object | plot_var_part_pq |
| Volcano plot for differential abundance results | plot_volcano_pq |
| Recluster sequences of an object of class 'physeq' or a list of DNA sequences | asv2otu postcluster_pq |
| Hill diversity profile for a phyloseq object | profile_hill_pq |
| Build a sample information tibble from physeq object | psmelt_samples_pq |
| Rarefy a phyloseq object to even sequencing depth | rarefy_even_depth_pq |
| Rarefy a phyloseq object | rarefy_pq |
| Rarefy (equalize) the number of samples per modality of a factor | rarefy_sample_count_by_modality |
| Read phyloseq object from multiple csv tables and a phylogenetic tree in Newick format. | read_pq |
| Rename the samples of a phyloseq slot | rename_samples |
| Rename samples of an otu_table | rename_samples_otu_table |
| Reorder fill and color scales to maximize perceptual contrast between adjacent segments | reorder_distinct_colors |
| Reorder taxa in otu_table/tax_table/refseq slot of a phyloseq object | reorder_taxa_pq |
| Reshape a ggplot2 object by wrapping its text elements | reshape_ggplot |
| Resolve conflict in a vector of taxonomy values | resolve_vector_ranks |
| Ridge plot of a phyloseq object | ridges_pq |
| Ridges plot of sample distribution across taxa | ridges_sam_pq |
| rotl wrapper for phyloseq data | rotl_pq |
| Match sample names from sam_data and fastq files | sam_data_matching_names |
| Load sample data from file and rename samples using names of samples and an optional order | sample_data_with_new_names |
| Sankey plot of 'phyloseq-class' object | sankey_pq |
| A wrapper of write_pq to save in all three possible formats | save_pq |
| Search for exact matching of sequences | search_exact_seq_pq |
| Select one sample from a physeq object | select_one_sample |
| Select a subset of taxa in a specified order where possible | select_taxa select_taxa,otu_table,character-method select_taxa,phylo,character-method select_taxa,phyloseq,character-method select_taxa,sample_data,character-method select_taxa,taxonomyTable,character-method select_taxa,XStringSet,character-method |
| Filter ancombc_pq results | signif_ancombc |
| Simplify taxonomy by removing some unused characters such as "k__" | simplify_taxo |
| Scaling with ranked subsampling (SRS) curve of phyloseq object | SRS_curve_pq |
| Scaling with Ranked Subsampling (SRS) normalization of a phyloseq object | srs_pq |
| Strength of species-group associations for a phyloseq object | strassoc_pq |
| Subsample a fastq file copying the n_seq first sequences in a given folder | subsample_fastq |
| Subset samples using a conditional boolean vector. | subset_samples_pq |
| Subset taxa using a conditional named boolean vector. | subset_taxa_pq |
| Subset taxa using a taxa control or distribution based method | subset_taxa_tax_control |
| Summarize a 'phyloseq-class' object using a plot. | summary_plot_pq |
| Re-cluster sequences of an object of class 'physeq' or cluster a list of DNA sequences using SWARM | swarm_clustering |
| Plot the distribution of sequences or ASV in one taxonomic levels | tax_bar_pq |
| Make a datatable with the taxonomy of a 'phyloseq-class' object | tax_datatable |
| Force taxa to be in columns in the otu_table of a physeq object | taxa_as_columns |
| Force taxa to be in columns in the otu_table of a physeq object | taxa_as_rows |
| Show taxa which are present in only one given level of a modality | taxa_only_in_one_level |
| Summarize information from sample data in a table | tbl_sum_samdata |
| Summarize a tax_table (taxonomic slot of phyloseq object) using gtsummary | tbl_sum_taxtable |
| This tutorial explores the dataset from Tengeler et al. (2020) available in the 'mia' package. obtained using 'mia::makePhyloseqFromTreeSE(Tengeler2020)' | Tengeler2020_pq |
| Trimmed Mean of M-values (TMM) normalization of a phyloseq object | tmm_pq |
| Track the number of reads (= sequences), samples and cluster (e.g. ASV) from various objects including dada-class and derep-class. | track_wkflow |
| Track the number of reads (= sequences), samples and cluster (e.g. ASV) for each sample | track_wkflow_samples |
| Unified dispatcher for all OTU-table transformations and normalisations | transform_pq |
| Adds transparency to a vector of colors | transp |
| Plot treemap of 2 taxonomic levels | treemap_pq |
| Compute tSNE position of samples from a phyloseq object | tsne_pq |
| Computes a manifold approximation and projection (UMAP) for phyloseq object | umap_pq |
| Get the unique value in x or NA if none | unique_or_na unique_or_na.default unique_or_na.factor |
| Default patterns for unwanted taxonomic values | unwanted_tax_patterns |
| Make upset plot for phyloseq object. | upset_pq |
| Test for differences between intersections | upset_test_pq |
| Partition the Variation of a phyloseq object by 2, 3, or 4 Explanatory Matrices | var_par_pq |
| Partition the Variation of a phyloseq object with rarefaction permutations | var_par_rarperm_pq |
| Venn diagram of 'phyloseq-class' object | venn_pq |
| Verify the validity of a phyloseq object | verify_pq |
| Verify the taxonomy table of a phyloseq object | verify_tax_table |
| Search for a list of sequence in a fasta file against physeq reference sequences using vsearch | vs_search_global |
| Recluster sequences of an object of class 'physeq' or cluster a list of DNA sequences using vsearch software | vsearch_clustering |
| Variance Stabilizing Transformation of a phyloseq object (DESeq2) | vst_pq |
| Wheat plot of a numeric distribution | wheat_plot |
| Save phyloseq object in the form of multiple csv tables. | write_pq |
